<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<title>MolTK C++ API: C:/Users/cmbruns/svn/moltk/c++/include/moltk/Aligner.h Source File</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>
<link href="doxygen.css" rel="stylesheet" type="text/css" />

<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
  $(document).ready(function() { searchBox.OnSelectItem(0); });
</script>

</head>
<body>
<div id="top"><!-- do not remove this div! -->


<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  
  <td id="projectlogo"><img alt="Logo" src="moltk55.png"/></td>
  
  
  <td style="padding-left: 0.5em;">
   <div id="projectname">MolTK C++ API
   &#160;<span id="projectnumber">0.3.0</span>
   </div>
   
  </td>
  
  
  
 </tr>
 </tbody>
</table>
</div>

<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
  <div id="navrow1" class="tabs">
    <ul class="tablist">
      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
      <li><a href="annotated.html"><span>Classes</span></a></li>
      <li class="current"><a href="files.html"><span>Files</span></a></li>
      <li>
        <div id="MSearchBox" class="MSearchBoxInactive">
        <span class="left">
          <img id="MSearchSelect" src="search/mag_sel.png"
               onmouseover="return searchBox.OnSearchSelectShow()"
               onmouseout="return searchBox.OnSearchSelectHide()"
               alt=""/>
          <input type="text" id="MSearchField" value="Search" accesskey="S"
               onfocus="searchBox.OnSearchFieldFocus(true)" 
               onblur="searchBox.OnSearchFieldFocus(false)" 
               onkeyup="searchBox.OnSearchFieldChange(event)"/>
          </span><span class="right">
            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
          </span>
        </div>
      </li>
    </ul>
  </div>
  <div id="navrow2" class="tabs2">
    <ul class="tablist">
      <li><a href="files.html"><span>File&#160;List</span></a></li>
      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
    </ul>
  </div>
<div class="header">
  <div class="headertitle">
<div class="title">C:/Users/cmbruns/svn/moltk/c++/include/moltk/Aligner.h</div>  </div>
</div>
<div class="contents">
<a href="Aligner_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00020"></a>00020 <span class="comment">*/</span>
<a name="l00021"></a>00021 
<a name="l00022"></a>00022 <span class="preprocessor">#ifndef MOLTK_ALIGN_ALIGNER_H</span>
<a name="l00023"></a>00023 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ALIGN_ALIGNER_H</span>
<a name="l00024"></a>00024 <span class="preprocessor"></span>
<a name="l00025"></a>00025 <span class="preprocessor">#include &lt;iostream&gt;</span>
<a name="l00026"></a>00026 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00027"></a>00027 <span class="preprocessor">#include &quot;<a class="code" href="Alignment_8h.html">moltk/Alignment.h</a>&quot;</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &quot;<a class="code" href="units_8h.html">moltk/units.h</a>&quot;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &quot;<a class="code" href="Biosequence_8h.html">moltk/Biosequence.h</a>&quot;</span>
<a name="l00030"></a>00030 
<a name="l00031"></a><a class="code" href="namespacemoltk.html">00031</a> <span class="keyword">namespace </span>moltk {
<a name="l00032"></a>00032 
<a name="l00034"></a><a class="code" href="classmoltk_1_1Aligner.html">00034</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1Aligner.html" title="Aligner is the class that creates sequence or structure alignments.">Aligner</a> 
<a name="l00035"></a>00035 {
<a name="l00036"></a>00036 <span class="keyword">public</span>:
<a name="l00037"></a>00037     <span class="comment">// Inner classes and typedefs first, then Aligner methods.</span>
<a name="l00038"></a>00038 
<a name="l00039"></a><a class="code" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">00039</a>     <span class="keyword">typedef</span> <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a>;
<a name="l00040"></a>00040 
<a name="l00041"></a>00041 
<a name="l00043"></a><a class="code" href="classmoltk_1_1Aligner_1_1Position.html">00043</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Aligner_1_1Position.html" title="Aligner::Position represents a special biosequence residue that knows how to score itself during alig...">Position</a>
<a name="l00044"></a>00044     {
<a name="l00045"></a>00045         <span class="keyword">public</span>:
<a name="l00046"></a>00046             <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html" title="Aligner::Position represents a special biosequence residue that knows how to score itself during alig...">Position</a>* <a class="code" href="classmoltk_1_1Aligner_1_1Position.html#a34f4a85b4fd078f833f1c091fd629b2c">clone</a>() <span class="keyword">const</span> = 0;
<a name="l00047"></a><a class="code" href="classmoltk_1_1Aligner_1_1Position.html#a71e3fa5525ce82fc0a501d7ae2ce5803">00047</a>             <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html#a71e3fa5525ce82fc0a501d7ae2ce5803">~Position</a>() {}
<a name="l00048"></a>00048             <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html#abee26ee88b3c4b037a19c4f1dff749a4">score</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html" title="Aligner::Position represents a special biosequence residue that knows how to score itself during alig...">Position</a>&amp; rhs) <span class="keyword">const</span> = 0;
<a name="l00049"></a>00049             <span class="keyword">virtual</span> <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html#adeb85b03da1c7a2101ca10548acf8e34">getOneLetterCode</a>() <span class="keyword">const</span> = 0;
<a name="l00050"></a>00050             <span class="comment">// Gap penalties are for inserting a gap character after this position.</span>
<a name="l00051"></a>00051             <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html#aed5476e1cfb4623e7bb65a713141eb67">gapOpenPenalty</a>() <span class="keyword">const</span> = 0;
<a name="l00052"></a>00052             <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html#aa896a3102ef9d955b5a43b431f98a712">gapExtensionPenalty</a>() <span class="keyword">const</span> = 0;
<a name="l00053"></a>00053     };
<a name="l00054"></a>00054 
<a name="l00055"></a>00055 
<a name="l00058"></a><a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html">00058</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html" title="Aligner::PositionList is a special sequence containing Aligner::Positions, which know how to score th...">PositionList</a> : <span class="keyword">public</span> std::vector&lt;Position*&gt;
<a name="l00059"></a>00059     {
<a name="l00060"></a>00060     <span class="keyword">public</span>:
<a name="l00061"></a><a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html#a7f3325aa682fd4f510b130f1b3c453ab">00061</a>         <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html#a7f3325aa682fd4f510b130f1b3c453ab">PositionList</a>() {}
<a name="l00062"></a>00062         <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html#a7f3325aa682fd4f510b130f1b3c453ab">PositionList</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html" title="Aligner::PositionList is a special sequence containing Aligner::Positions, which know how to score th...">PositionList</a>&amp; rhs);
<a name="l00063"></a>00063         <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html#a51d9dc02420d4c9b8177705feea15467">~PositionList</a>();
<a name="l00064"></a>00064         <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html" title="Aligner::PositionList is a special sequence containing Aligner::Positions, which know how to score th...">PositionList</a>&amp; <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html#a23e16dfb25bddd119f7794248a0cb62d">operator=</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html" title="Aligner::PositionList is a special sequence containing Aligner::Positions, which know how to score th...">PositionList</a>&amp; rhs);
<a name="l00065"></a>00065     };
<a name="l00066"></a>00066 
<a name="l00067"></a>00067 
<a name="l00070"></a><a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html">00070</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html" title="Aligner::Scorer converts dumb sequence and structure residues into Aligner::Positions, which know how to quickly score themselves with other AlignerPositions.">Scorer</a>
<a name="l00071"></a>00071     {
<a name="l00072"></a>00072     <span class="keyword">public</span>:
<a name="l00073"></a><a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#acdd1d2e2c6d447444eba9155ff92f07b">00073</a>         <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#acdd1d2e2c6d447444eba9155ff92f07b">Scorer</a>() : <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a13c168f654fe7cf08b690e3d670101b1">endGapsFree</a>(true) {}
<a name="l00074"></a>00074         <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html" title="Aligner::Position represents a special biosequence residue that knows how to score itself during alig...">Aligner::Position</a>* <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#af2479b1b2399472832af088870a37c5e">createPosition</a>(<span class="keywordtype">char</span> sequenceLetter, <span class="keywordtype">bool</span> bTerminus = <span class="keyword">false</span>) <span class="keyword">const</span> = 0;
<a name="l00075"></a>00075         <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1Aligner_1_1Position.html" title="Aligner::Position represents a special biosequence residue that knows how to score itself during alig...">Aligner::Position</a>* <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#af2479b1b2399472832af088870a37c5e">createPosition</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment_1_1Column.html">Alignment::Column</a>&amp;, <span class="keywordtype">bool</span> bTerminus = <span class="keyword">false</span>) <span class="keyword">const</span> = 0;
<a name="l00076"></a><a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#ae7957680cdfe5d2d06475f0b8d5f6741">00076</a>         <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#ae7957680cdfe5d2d06475f0b8d5f6741">getEndGapsFree</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a13c168f654fe7cf08b690e3d670101b1">endGapsFree</a>;}
<a name="l00077"></a><a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a0e1bd3b736dbaf8c3a890f66f176c9ec">00077</a>         <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a0e1bd3b736dbaf8c3a890f66f176c9ec">setEndGapsFree</a>(<span class="keywordtype">bool</span> f) {<a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a13c168f654fe7cf08b690e3d670101b1">endGapsFree</a> = f;}
<a name="l00078"></a>00078 
<a name="l00079"></a>00079     <span class="keyword">protected</span>:
<a name="l00080"></a><a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a13c168f654fe7cf08b690e3d670101b1">00080</a>         <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a13c168f654fe7cf08b690e3d670101b1">endGapsFree</a>;
<a name="l00081"></a>00081     };
<a name="l00082"></a>00082 
<a name="l00084"></a><a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55b">00084</a>     <span class="keyword">enum</span> <a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55b" title="TracebackPointer is an Aligner::Cell attribute that helps reconstruct the final alignment.">TracebackPointer</a>
<a name="l00085"></a>00085     {
<a name="l00086"></a><a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba6da2cb4f6502904671847ec848503045">00086</a>         <a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba6da2cb4f6502904671847ec848503045">TRACEBACK_UP</a>,
<a name="l00087"></a><a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bae1838f55d1bd7835d79ffee07b42467e">00087</a>         <a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bae1838f55d1bd7835d79ffee07b42467e">TRACEBACK_UPLEFT</a>,
<a name="l00088"></a><a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bab5353821ddae5b7ea5c6ce44d2d62d81">00088</a>         <a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bab5353821ddae5b7ea5c6ce44d2d62d81">TRACEBACK_LEFT</a>,
<a name="l00089"></a><a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55baed40c1c6e565bbbee48d601aaafe0812">00089</a>         <a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55baed40c1c6e565bbbee48d601aaafe0812">TRACEBACK_DONE</a>,
<a name="l00090"></a><a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba4de2c99df6a5314ce86b8d850734d220">00090</a>         <a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba4de2c99df6a5314ce86b8d850734d220">TRACEBACK_NOT_INITIALIZED</a>
<a name="l00091"></a>00091     };
<a name="l00092"></a>00092 
<a name="l00093"></a>00093 
<a name="l00095"></a><a class="code" href="classmoltk_1_1Aligner_1_1Cell.html">00095</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Aligner_1_1Cell.html" title="An Aligner::Cell is one node in the dynamic programming table.">Cell</a>
<a name="l00096"></a>00096     {
<a name="l00097"></a>00097     <span class="keyword">public</span>:
<a name="l00098"></a>00098         <a class="code" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55b" title="TracebackPointer is an Aligner::Cell attribute that helps reconstruct the final alignment.">TracebackPointer</a> <a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#a46afa907bfe05f49dec3a49ec22cb9ef">compute_traceback_pointer</a>() <span class="keyword">const</span>;
<a name="l00099"></a>00099         <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#ad8b6f514f6420389c670370687518fb4">compute_v</a>() <span class="keyword">const</span>;
<a name="l00100"></a>00100 
<a name="l00101"></a>00101         <span class="comment">// Gusfield nomenclature</span>
<a name="l00102"></a><a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#aa766a462abc1caa6199a66ca3a37ca68">00102</a>         <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#aa766a462abc1caa6199a66ca3a37ca68" title="V, best score through this cell.">v</a>; 
<a name="l00103"></a><a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#ac66f132d15e84f948a4b041d78c56f03">00103</a>         <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#ac66f132d15e84f948a4b041d78c56f03" title="G, best ungapped score through this cell.">g</a>; 
<a name="l00104"></a><a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#abc2eef27dee7e7042069ea25c049dd5f">00104</a>         <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#abc2eef27dee7e7042069ea25c049dd5f" title="E, best score with gap in sequence 1.">e</a>; 
<a name="l00105"></a><a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#adbf73e205dd0a1ba60a232987058da50">00105</a>         <a class="code" href="structmoltk_1_1units_1_1quantity.html" title="For efficiency, quantity&lt;&gt; should compile to a double in C++.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Aligner_1_1Cell.html#adbf73e205dd0a1ba60a232987058da50" title="F, best score with gap in sequence 2.">f</a>; 
<a name="l00106"></a>00106     };
<a name="l00107"></a><a class="code" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">00107</a>     <span class="keyword">typedef</span> std::vector&lt;Cell&gt; <a class="code" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">DpRow</a>;
<a name="l00108"></a><a class="code" href="classmoltk_1_1Aligner.html#a8c586048912c20d16e8446694019f412">00108</a>     <span class="keyword">typedef</span> std::vector&lt;DpRow&gt; <a class="code" href="classmoltk_1_1Aligner.html#a8c586048912c20d16e8446694019f412">DpTable</a>;
<a name="l00109"></a>00109 
<a name="l00110"></a>00110 
<a name="l00111"></a>00111     <span class="comment">// Aligner::Stage represents current state of an incomplete alignment</span>
<a name="l00112"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208">00112</a>     <span class="keyword">enum</span> <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208">Stage</a> {
<a name="l00113"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a7253e4f0fe5c7b9e10c0f4c2cfa44a37">00113</a>         <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a7253e4f0fe5c7b9e10c0f4c2cfa44a37">EMPTY_STAGE</a>, <span class="comment">// have nothing</span>
<a name="l00114"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208abe28a2050abcd2402e7b5cb421fdad12">00114</a>         <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208abe28a2050abcd2402e7b5cb421fdad12">SCORER_STAGE</a>, <span class="comment">// have a scorer</span>
<a name="l00115"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208abf5f1602c88dd0756aca9c14d86f95d1">00115</a>         <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208abf5f1602c88dd0756aca9c14d86f95d1">SEQUENCE_STAGE</a>, <span class="comment">// have sequences</span>
<a name="l00116"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208af2738aeda664e92c2a24dcc36a606400">00116</a>         <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208af2738aeda664e92c2a24dcc36a606400">ALLOCATED_STAGE</a>, <span class="comment">// have dynamic programming table</span>
<a name="l00117"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a622c31a2537063f9018565e194ed2306">00117</a>         <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a622c31a2537063f9018565e194ed2306">TABLE_INITIALIZED_STAGE</a>, <span class="comment">// first edge of table initialized</span>
<a name="l00118"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a17726bca901d203d6ed01e5ff0072a6e">00118</a>         <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a17726bca901d203d6ed01e5ff0072a6e">RECURRENCE_COMPUTED_STAGE</a>, <span class="comment">// recurrence computed</span>
<a name="l00119"></a><a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208af3f1f98ed3b0cf9c314f1baacfb7ce33">00119</a>         <a class="code" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208af3f1f98ed3b0cf9c314f1baacfb7ce33">TRACED_STAGE</a> <span class="comment">// alignment computed</span>
<a name="l00120"></a>00120     };
<a name="l00121"></a>00121 
<a name="l00122"></a>00122 
<a name="l00123"></a>00123 <span class="keyword">public</span>:
<a name="l00124"></a>00124     <span class="comment">// Finally, the actual Aligner methods</span>
<a name="l00125"></a>00125     <a class="code" href="classmoltk_1_1Aligner.html#a99008604e446e2adc4f0df7e4afd6c9e">Aligner</a>();
<a name="l00126"></a>00126     <span class="comment">// Alignment align(const Alignment&amp;);</span>
<a name="l00127"></a>00127     <a class="code" href="classmoltk_1_1Alignment.html">Alignment</a> <a class="code" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment.html">Alignment</a>&amp;, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment.html">Alignment</a>&amp;);
<a name="l00128"></a>00128 
<a name="l00129"></a>00129     <span class="keyword">static</span> <span class="keyword">const</span> Scorer&amp; <a class="code" href="classmoltk_1_1Aligner.html#ae3a1f399e1088bc30da6bdb7c1cec868">getDefaultScorer</a>();
<a name="l00130"></a><a class="code" href="classmoltk_1_1Aligner.html#a674defbb5c8ee8538f506201ec8322a2">00130</a>     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1Aligner.html#a674defbb5c8ee8538f506201ec8322a2">getEndGapsFree</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae">scorer</a>-&gt;<a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#ae7957680cdfe5d2d06475f0b8d5f6741">getEndGapsFree</a>();}
<a name="l00131"></a><a class="code" href="classmoltk_1_1Aligner.html#a18de26cff90bcb2400996bea4cfa5d3b">00131</a>     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a18de26cff90bcb2400996bea4cfa5d3b">setEndGapsFree</a>(<span class="keywordtype">bool</span> f) {<a class="code" href="classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae">scorer</a>-&gt;<a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html#a0e1bd3b736dbaf8c3a890f66f176c9ec">setEndGapsFree</a>(f);}
<a name="l00132"></a>00132 
<a name="l00133"></a>00133 <span class="keyword">protected</span>:
<a name="l00134"></a>00134     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a5a7bc14266d9a09c00133aeee98ae039">init</a>();
<a name="l00135"></a>00135     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a5a7bc14266d9a09c00133aeee98ae039">init</a>(<span class="keyword">const</span> PositionList&amp; seq1Param, <span class="keyword">const</span> PositionList&amp; seq2Param);
<a name="l00136"></a>00136     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#ae88d9a29786521dacbf511a8097bb063">allocate_dp_table</a>();
<a name="l00137"></a>00137     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a00167b2c4ea9d0e01e5ed56e8946b713">initialize_dp_table</a>();
<a name="l00138"></a>00138     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a47aa0cc272a3aa95d23dfec38d7883b0">initialize_dp_row</a>(<span class="keywordtype">size_t</span> rowIndex, <a class="code" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">DpRow</a>&amp; row);
<a name="l00139"></a>00139     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a66756b5e61b63ee8f26b6abb7b1de02e">compute_recurrence</a>();
<a name="l00140"></a>00140     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a38863ca0eb76e0241abedefaa69b0048">compute_cell_recurrence</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
<a name="l00141"></a>00141     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a5c0dfb557f1fe73f8b0b6dc6eb029ab2">compute_cell_recurrence_freeE</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
<a name="l00142"></a>00142     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#ac1c097af307968d9caf76242977a288d">compute_cell_recurrence_freeF</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
<a name="l00143"></a>00143     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Aligner.html#a8d28c9bb018c6d4913e305c36093eeb0">compute_cell_recurrence_freeEF</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
<a name="l00144"></a>00144     <a class="code" href="classmoltk_1_1Alignment.html">Alignment</a> <a class="code" href="classmoltk_1_1Aligner.html#ac6170833b8d8c742719e45186aff85b8">compute_traceback</a>();
<a name="l00145"></a>00145 
<a name="l00146"></a>00146     <span class="comment">// Information gapOpenPenalty; // positive penalty (will be subtracted at gaps)</span>
<a name="l00147"></a>00147     <span class="comment">// Information gapExtensionPenalty; // positive penalty (will be subtracted on extension)</span>
<a name="l00148"></a>00148     <span class="comment">// bool bEndGapsFree;</span>
<a name="l00149"></a><a class="code" href="classmoltk_1_1Aligner.html#a3aef8f8a287ee4881e5a981e379ecf7d">00149</a>     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1Aligner.html#a3aef8f8a287ee4881e5a981e379ecf7d">bLocalAligner</a>;
<a name="l00150"></a><a class="code" href="classmoltk_1_1Aligner.html#afedcb89907a4037bccb3754a6e2eb2a3">00150</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Aligner.html#afedcb89907a4037bccb3754a6e2eb2a3">m</a>; <span class="comment">// length of sequence 1</span>
<a name="l00151"></a><a class="code" href="classmoltk_1_1Aligner.html#a3ee7cf4bee96c010e3644615f45f7dcc">00151</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Aligner.html#a3ee7cf4bee96c010e3644615f45f7dcc">n</a>; <span class="comment">// length of sequence 2</span>
<a name="l00152"></a><a class="code" href="classmoltk_1_1Aligner.html#a3e56bf282680824b74a59506f91f93d9">00152</a>     <a class="code" href="classmoltk_1_1Aligner.html#a8c586048912c20d16e8446694019f412">DpTable</a> <a class="code" href="classmoltk_1_1Aligner.html#a3e56bf282680824b74a59506f91f93d9">dpTable</a>;
<a name="l00153"></a><a class="code" href="classmoltk_1_1Aligner.html#ac285f6a9ad3b9652ef20933e54fc0d21">00153</a>     <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html" title="Aligner::PositionList is a special sequence containing Aligner::Positions, which know how to score th...">PositionList</a> <a class="code" href="classmoltk_1_1Aligner.html#ac285f6a9ad3b9652ef20933e54fc0d21">seq1</a>;
<a name="l00154"></a><a class="code" href="classmoltk_1_1Aligner.html#a5358527ccea8ec4afca70a74abe043f9">00154</a>     <a class="code" href="classmoltk_1_1Aligner_1_1PositionList.html" title="Aligner::PositionList is a special sequence containing Aligner::Positions, which know how to score th...">PositionList</a> <a class="code" href="classmoltk_1_1Aligner.html#a5358527ccea8ec4afca70a74abe043f9">seq2</a>;
<a name="l00155"></a><a class="code" href="classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae">00155</a>     <a class="code" href="classmoltk_1_1Aligner_1_1Scorer.html" title="Aligner::Scorer converts dumb sequence and structure residues into Aligner::Positions, which know how to quickly score themselves with other AlignerPositions.">Scorer</a>* <a class="code" href="classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae">scorer</a>;
<a name="l00156"></a><a class="code" href="classmoltk_1_1Aligner.html#ab2cbd165a86522352756f28b0231e7a2">00156</a>     <a class="code" href="classmoltk_1_1Alignment.html">Alignment</a> <a class="code" href="classmoltk_1_1Aligner.html#ab2cbd165a86522352756f28b0231e7a2">alignment</a>;
<a name="l00157"></a>00157 };
<a name="l00158"></a>00158 
<a name="l00159"></a>00159 } <span class="comment">// namespace moltk</span>
<a name="l00160"></a>00160 
<a name="l00161"></a>00161 <span class="preprocessor">#endif // MOLTK_ALIGN_ALIGNER_H</span>
<a name="l00162"></a>00162 <span class="preprocessor"></span>
</pre></div></div>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a></div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>



<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.7.5.1
</small></address>

</body>
</html>
